1
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Mondal P, Cazade PA, Das AK, Bereau T, Meuwly M. Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer. J Phys Chem B 2021; 125:10928-10938. [PMID: 34559531 DOI: 10.1021/acs.jpcb.1c05423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm-1 from the PC, 13 cm-1 from the MTP, and 47 cm-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ02 from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)3. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ02 is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including PII, β, αR, and αL), whereas that covered by the MTP-based simulations is dominated by PII with some contributions from β and αR. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Akshaya K Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Tristan Bereau
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland.,Department of Chemistry, Brown University, Providence/RI 02912, United States
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2
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Gardner AM, Gardner PR. Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin. J Biol Chem 2020; 296:100186. [PMID: 33310705 PMCID: PMC7948479 DOI: 10.1074/jbc.ra120.016637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
The substrates O2 and NO cooperatively activate the NO dioxygenase function of Escherichia coli flavohemoglobin. Steady-state and transient kinetic measurements support a structure-based mechanistic model in which O2 and NO movements and conserved amino acids at the E11, G8, E2, E7, B10, and F7 positions within the globin domain control activation. In the cooperative and allosteric mechanism, O2 migrates to the catalytic heme site via a long hydrophobic tunnel and displaces LeuE11 away from the ferric iron, which forces open a short tunnel to the catalytic site gated by the ValG8/IleE15 pair and LeuE11. NO permeates this tunnel and leverages upon the gating side chains triggering the CD loop to furl, which moves the E and F-helices and switches an electron transfer gate formed by LysF7, GlnE7, and water. This allows FADH2 to reduce the ferric iron, which forms the stable ferric–superoxide–TyrB10/GlnE7 complex. This complex reacts with internalized NO with a bimolecular rate constant of 1010 M−1 s−1 forming nitrate, which migrates to the CD loop and unfurls the spring-like structure. To restart the cycle, LeuE11 toggles back to the ferric iron. Actuating electron transfer with O2 and NO movements averts irreversible NO poisoning and reductive inactivation of the enzyme. Together, structure snapshots and kinetic constants provide glimpses of intermediate conformational states, time scales for motion, and associated energies.
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Affiliation(s)
- Anne M Gardner
- Research and Development Division, Miami Valley Biotech, Dayton, Ohio, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Paul R Gardner
- Research and Development Division, Miami Valley Biotech, Dayton, Ohio, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Chemistry and Biochemistry Department, University of Dayton, Dayton, Ohio, USA.
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3
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Giordano D, Pesce A, Vermeylen S, Abbruzzetti S, Nardini M, Marchesani F, Berghmans H, Seira C, Bruno S, Javier Luque F, di Prisco G, Ascenzi P, Dewilde S, Bolognesi M, Viappiani C, Verde C. Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions. Comput Struct Biotechnol J 2020; 18:2132-2144. [PMID: 32913582 PMCID: PMC7451756 DOI: 10.1016/j.csbj.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/10/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
While the functions of the recently discovered cytoglobin, ubiquitously expressed in vertebrate tissues, remain uncertain, Antarctic fish provide unparalleled models to study novel protein traits that may arise from cold adaptation. We report here the spectral, ligand-binding and enzymatic properties (peroxynitrite isomerization, nitrite-reductase activity) of cytoglobin-1 from two Antarctic fish, Chaenocephalus aceratus and Dissostichus mawsoni, and present the crystal structure of D. mawsoni cytoglobin-1. The Antarctic cytoglobins-1 display high O2 affinity, scarcely compatible with an O2-supply role, a slow rate constant for nitrite-reductase activity, and do not catalyze peroxynitrite isomerization. Compared with mesophilic orthologues, the cold-adapted cytoglobins favor binding of exogenous ligands to the hexa-coordinated bis-histidyl species, a trait related to their higher rate constant for distal-His/heme-Fe dissociation relative to human cytoglobin. At the light of a remarkable 3D-structure conservation, the observed differences in ligand-binding kinetics may reflect Antarctic fish cytoglobin-1 specific features in the dynamics of the heme distal region and of protein matrix cavities, suggesting adaptation to functional requirements posed by the cold environment. Taken together, the biochemical and biophysical data presented suggest that in Antarctic fish, as in humans, cytoglobin-1 unlikely plays a role in O2 transport, rather it may be involved in processes such as NO detoxification.
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Key Words
- C.aceCygb-1*, Mutant of C.aceCygb-1
- C.aceCygb-1, Cytoglobin-1 of C. aceratus
- CO, Carbon monoxide
- CYGB, Human Cygb
- Cold-adaptation
- Cygb, Cytoglobin
- Cygb-1, Cytoglobin 1
- Cygb-2, Cytoglobin 2
- Cygbh, Hexa-coordinated bis-histidyl species
- Cygbp, Penta-coordinated Cygb
- Cytoglobin
- D.mawCygb-1*, Mutant of D.mawCygb-1
- D.mawCygb-1, Cytoglobin-1 of D. mawsoni
- DTT, Dithiothreitol
- Hb, Hemoglobin
- Ligand properties
- MD, Molecular Dynamics
- Mb, Myoglobin
- NGB, Human neuroglobin
- NO dioxygenase
- NO, Nitric oxide
- RNS, Reactive Nitrogen Species
- ROS, Reactive Oxygen Species
- X-ray structure
- p50, O2 partial pressure required to achieve half saturation
- rms, Root-mean square
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, I-16121 Genova, Italy
| | - Stijn Vermeylen
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Francesco Marchesani
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Constantí Seira
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
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4
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Bringas M, Lombardi LE, Luque FJ, Estrin DA, Capece L. Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations. Chemphyschem 2019; 20:2451-2460. [PMID: 31365183 DOI: 10.1002/cphc.201900589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/30/2019] [Indexed: 11/07/2022]
Abstract
Computer simulation studies of the molecular basis for ligand migration in proteins allow the description of key events such as the transition between docking sites, displacement of existing ligands and solvent molecules, and open/closure of specific "gates", among others. In heme proteins, ligand migration from the solvent to the active site preludes the binding to the heme iron and triggers different functions. In this work, molecular dynamics simulations, a Markov State Model of migration and empirical kinetic equations are combined to study the migration of O2 and NO in two truncated hemoglobins of Mycobacterium tuberculosis (Mt-TrHbN and Mt-TrHbO). For Mt-TrHbN, we show that the difference in the association constant in the oxy and deoxy states relies mainly in the displacement of water molecules anchored in the distal cavity in the deoxy form. The results here provide a valuable approach to study ligand migration in globins.
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Affiliation(s)
- Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.,Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Buenos Aires, Argentina
| | - Leandro E Lombardi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires - CONICET, C1428EGA, Buenos Aires, Argentina
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences, University of Barcelona, Campus Torribera, 08921, Santa Coloma de Gramenet, Spain.,Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028, Barcelona, Spain
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.,Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Buenos Aires, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.,Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Buenos Aires, Argentina
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5
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Das AK, Meuwly M. Kinetic Analysis and Structural Interpretation of Competitive Ligand Binding for NO Dioxygenation in Truncated Hemoglobin N. Angew Chem Int Ed Engl 2018; 57:3509-3513. [PMID: 29356324 DOI: 10.1002/anie.201711445] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Indexed: 11/06/2022]
Abstract
The conversion of nitric oxide (NO) into nitrate (NO3- ) by dioxygenation protects cells from lethal NO. Starting from NO-bound heme, the first step in converting NO into benign NO3- is the ligand exchange reaction FeNO+O2 →FeO2 +NO, which is still poorly understood at a molecular level. For wild-type (WT) truncated hemoglobin N (trHbN) and its Y33A mutant, the calculated barriers for the exchange reaction differ by 1.5 kcal mol-1 , compared with 1.7 kcal mol-1 from experiment. It is directly confirmed that the ligand exchange reaction is rate-limiting in trHbN and that entropic contributions account for 75 % of the difference between the WT and the mutant. Residues Tyr 33, Phe 46, Val 80, His 81, and Gln 82 surrounding the active site are expected to control the reaction path. By comparison with electronic structure calculations, the transition state separating the two ligand-bound states was assigned to a 2 A state.
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Affiliation(s)
- Akshaya Kumar Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
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6
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Kinetische Analyse und strukturelle Interpretation der kompetitiven Ligandenbindung für Denitrifikation in gekürztem Hämoglobin N. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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El Hage K, Mondal P, Meuwly M. Free energy simulations for protein ligand binding and stability. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2017.1416115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel , Basel, Switzerland
| | - Padmabati Mondal
- Department of Chemistry, University of Basel , Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Basel, Switzerland
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8
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El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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9
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Diamantis P, Unke OT, Meuwly M. Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N. PLoS Comput Biol 2017; 13:e1005450. [PMID: 28358830 PMCID: PMC5391117 DOI: 10.1371/journal.pcbi.1005450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 04/13/2017] [Accepted: 03/13/2017] [Indexed: 11/18/2022] Open
Abstract
In heme proteins, the efficient transport of ligands such as NO or O2 to the binding site is achieved via ligand migration networks. A quantitative assessment of ligand diffusion in these networks is thus essential for a better understanding of the function of these proteins. For this, Xe migration in truncated hemoglobin N (trHbN) of Mycobacterium Tuberculosis was studied using molecular dynamics simulations. Transitions between pockets of the migration network and intra-pocket relaxation occur on similar time scales (10 ps and 20 ps), consistent with low free energy barriers (1-2 kcal/mol). Depending on the pocket from where Xe enters a particular transition, the conformation of the side chains lining the transition region differs which highlights the coupling between ligand and protein degrees of freedom. Furthermore, comparison of transition probabilities shows that Xe migration in trHbN is a non-Markovian process. Memory effects arise due to protein rearrangements and coupled dynamics as Xe moves through it. Binding and transport of ligands in proteins is essential, in particular in globular proteins which often exhibit internal cavities. In truncated Hemoglobin N (trHbN) these cavities are arranged as a network with particular connectivities. The present work supports the notion that ligand diffusion in trHbN is an active process and coupled to the protein dynamics. Furthermore, transition probabilities between neighboring pockets depend on the location from where the ligand entered the transition, which is typical for non-Markovian processes. Hence, ligand migration in trHbN exhibits memory effects due to dynamical coupling between the protein and ligand motion.
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Affiliation(s)
| | - Oliver T. Unke
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
- * E-mail:
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10
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McLean KJ, Munro AW. Drug targeting of heme proteins in Mycobacterium tuberculosis. Drug Discov Today 2016; 22:566-575. [PMID: 27856345 DOI: 10.1016/j.drudis.2016.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/28/2016] [Accepted: 11/02/2016] [Indexed: 01/08/2023]
Abstract
TB, caused by the human pathogen Mycobacterium tuberculosis (Mtb), causes more deaths than any other infectious disease. Iron is crucial for Mtb to infect the host and to sustain infection, with Mtb encoding large numbers of iron-binding proteins. Many of these are hemoproteins with key roles, including defense against oxidative stress, cellular signaling and regulation, host cholesterol metabolism, and respiratory processes. Various heme enzymes in Mtb are validated drug targets and/or products of genes essential for bacterial viability or survival in the host. Here, we review the structure, function, and druggability of key Mtb heme enzymes and strategies used for their inhibition.
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Affiliation(s)
- Kirsty J McLean
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Andrew W Munro
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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11
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Bustamante JP, Szretter ME, Sued M, Martí MA, Estrin DA, Boechi L. A quantitative model for oxygen uptake and release in a family of hemeproteins. Bioinformatics 2016; 32:1805-13. [PMID: 27153569 DOI: 10.1093/bioinformatics/btw083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/30/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. RESULTS We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. CONTACT lboechi@ic.fcen.uba.ar SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - María E Szretter
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires Departamento De Matemática, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Mariela Sued
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Marcelo A Martí
- Departamento De Química Biológica E Instituto De Química Biológica De La Facultad De Ciencias Exactas Y Naturales (IQUIBICEN), Universidad De Buenos Aires, Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Leonardo Boechi
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
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12
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Koebke KJ, Waletzko MT, Pacheco AA. Direct Monitoring of the Reaction between Photochemically Generated Nitric Oxide and Mycobacterium tuberculosis Truncated Hemoglobin N Wild Type and Variant Forms: An Assessment of Computational Mechanistic Predictions. Biochemistry 2016; 55:686-96. [DOI: 10.1021/acs.biochem.5b01145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Michael T. Waletzko
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - A. Andrew Pacheco
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin 53211, United States
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13
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Cazade PA, Zheng W, Prada-Gracia D, Berezovska G, Rao F, Clementi C, Meuwly M. A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks. J Chem Phys 2015; 142:025103. [PMID: 25591387 DOI: 10.1063/1.4904431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k-means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.
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Affiliation(s)
- Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Wenwei Zheng
- Department of Chemistry, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - Diego Prada-Gracia
- School of Soft Matter Research, Freiburg Institute for Advanced Studies, Albertstrasse 19, 79104 Freiburg im Breisgau, Germany
| | - Ganna Berezovska
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Francesco Rao
- School of Soft Matter Research, Freiburg Institute for Advanced Studies, Albertstrasse 19, 79104 Freiburg im Breisgau, Germany
| | - Cecilia Clementi
- Department of Chemistry, Rice University, 6100 Main St., Houston, Texas 77005, USA
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Cazade PA, Hédin F, Xu ZH, Meuwly M. Vibrational relaxation and energy migration of N-methylacetamide in water: the role of nonbonded interactions. J Phys Chem B 2015; 119:3112-22. [PMID: 25581333 DOI: 10.1021/jp511701z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonequilibrium molecular dynamics (MD) simulations together with physics-based force fields are used to follow energy flow between vibrationally excited N-methylacetamide (NMA) and water. The simulations are carried out with a previously validated force field for NMA, based on a multipolar representation of the electrostatics, and with a new fluctuating point charge model. For the water solvent, a flexible and a rigid model was employed to distinguish between the role of inter- and intramolecular degrees of freedom. On a 10 ps time scale about 90% of the available energy goes into the solvent. The remaining energy resides within internal NMA-degrees of freedom from where energy flow takes place on longer time scales. The total amount of energy transferred to the solvent on the 10 ps time scale does not depend on whether the water molecules are rigid or flexible during the simulations. Vibrational energy relaxation time scales include two regimes: one on the several 100 fs time scale and a longer one, ranging from 6 to 10 ps. This longer time scale agrees with previous simulations but overestimates the experimentally determined relaxation time by a factor of 2, which can be explained by the classical treatment of the vibrations. Including a previously determined quantum correction factor brings the long time scale into quite favorable agreement with experiment. Coupling to the bending vibration of the water molecules in H-bonding contact with the excited C═O chromophore is substantial. The equilibrium and nonequilibrium distribution of the bending angles of the water molecules in contact with the local oscillator are non-Gaussian, and one approaches the other on the subpicosecond time scale. Analysis of the water velocity distribution suggests that the C═O vibrational energy relaxes into the solvent water shells in an impulsive fashion on a picosecond time scale.
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Affiliation(s)
- Pierre-André Cazade
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland
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15
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Cazade PA, Berezovska G, Meuwly M. Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks. Biochim Biophys Acta Gen Subj 2014; 1850:996-1005. [PMID: 25224733 DOI: 10.1016/j.bbagen.2014.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/01/2014] [Accepted: 09/03/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. METHODS All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. RESULTS Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. CONCLUSIONS Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. GENERAL SIGNIFICANCE Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland
| | - Ganna Berezovska
- Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80 4056 Basel, Switzerland; Department of Chemistry, Brown University, Providence/RI, USA.
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16
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Cazade PA, Bereau T, Meuwly M. Computational Two-Dimensional Infrared Spectroscopy without Maps: N-Methylacetamide in Water. J Phys Chem B 2014; 118:8135-47. [DOI: 10.1021/jp5011692] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pierre-André Cazade
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Tristan Bereau
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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Dellarole M, Roumestand C, Royer C, Lecomte JTJ. Volumetric properties underlying ligand binding in a monomeric hemoglobin: a high-pressure NMR study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1910-22. [PMID: 23619242 DOI: 10.1016/j.bbapap.2013.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 11/16/2022]
Abstract
The 2/2 hemoglobin of the cyanobacterium Synechococcus sp. PCC 7002, GlbN, coordinates the heme iron with two histidines and exists either with a b heme or with a covalently attached heme. The binding of exogenous ligands displaces the distal histidine and induces a conformational rearrangement involving the reorganization of internal void volumes. The formation of passageways within the resulting conformation is thought to facilitate ligand exchange and play a functional role. Here we monitored the perturbation induced by pressure on the ferric bis-histidine and cyanide-bound states of GlbN using (1)H-(15)N HSQC NMR spectroscopy. We inspected the outcome with a statistical analysis of 170 homologous 2/2 hemoglobin sequences. We found that the compression landscape of GlbN, as represented by the variation of an average chemical shift parameter, was highly sensitive to ligand swapping and heme covalent attachment. Stabilization of rare conformers was observed at high pressures and consistent with cavity redistribution upon ligand binding. In all states, the EF loop was found to be exceptionally labile to pressure, suggesting a functional role as a semi-flexible hinge between the adjacent helices. Finally, coevolved clusters presented a common pattern of compensating pressure responses. The high-pressure dissection combined with protein sequence analysis established locations with volumetric signatures relevant to residual communication of 2/2 hemoglobins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Mariano Dellarole
- Centre de Biochimie Structurale, CNRS, UMR 5048, Montpellier, France
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18
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Nienhaus K, Lutz S, Meuwly M, Nienhaus GU. Reaction-pathway selection in the structural dynamics of a heme protein. Chemistry 2013; 19:3558-62. [PMID: 23401035 DOI: 10.1002/chem.201203558] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 12/28/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
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Boechi L, Arrar M, Martí MA, Olson JS, Roitberg AE, Estrin DA. Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7. J Biol Chem 2013; 288:6754-62. [PMID: 23297402 DOI: 10.1074/jbc.m112.426056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis.
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Affiliation(s)
- Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física/Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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